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- EMDB-15485: Structure of the human DDB1-DCAF12 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-15485
TitleStructure of the human DDB1-DCAF12 complex
Map dataLocally sharpened map (LocScale).
Sample
  • Complex: Complex of DDB1-DCAF12
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DDB1- and CUL4-associated factor 12
Keywordsubiquitin / E3 / TRiC / chaperonin / LIGASE
Function / homology
Function and homology information


positive regulation by virus of viral protein levels in host cell / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / viral release from host cell / ectopic germ cell programmed cell death / ubiquitin-like ligase-substrate adaptor activity / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / T cell activation / regulation of autophagy / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Dual Incision in GG-NER / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / centrosome / DNA damage response / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / RSE1/DDB1/CPSF1 first beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / : / CPSF A subunit region / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...: / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / RSE1/DDB1/CPSF1 first beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / : / CPSF A subunit region / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsPla-Prats C / Cavadini S / Kempf G / Thoma NH
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: EMBO J / Year: 2023
Title: Recognition of the CCT5 di-Glu degron by CRL4 is dependent on TRiC assembly.
Authors: Carlos Pla-Prats / Simone Cavadini / Georg Kempf / Nicolas H Thomä /
Abstract: Assembly Quality Control (AQC) E3 ubiquitin ligases target incomplete or incorrectly assembled protein complexes for degradation. The CUL4-RBX1-DDB1-DCAF12 (CRL4 ) E3 ligase preferentially ...Assembly Quality Control (AQC) E3 ubiquitin ligases target incomplete or incorrectly assembled protein complexes for degradation. The CUL4-RBX1-DDB1-DCAF12 (CRL4 ) E3 ligase preferentially ubiquitinates proteins that carry a C-terminal double glutamate (di-Glu) motif. Reported CRL4 di-Glu-containing substrates include CCT5, a subunit of the TRiC chaperonin. How DCAF12 engages its substrates and the functional relationship between CRL4 and CCT5/TRiC is currently unknown. Here, we present the cryo-EM structure of the DDB1-DCAF12-CCT5 complex at 2.8 Å resolution. DCAF12 serves as a canonical WD40 DCAF substrate receptor and uses a positively charged pocket at the center of the β-propeller to bind the C-terminus of CCT5. DCAF12 specifically reads out the CCT5 di-Glu side chains, and contacts other visible degron amino acids through Van der Waals interactions. The CCT5 C-terminus is inaccessible in an assembled TRiC complex, and functional assays demonstrate that DCAF12 binds and ubiquitinates monomeric CCT5, but not CCT5 assembled into TRiC. Our biochemical and structural results suggest a previously unknown role for the CRL4 E3 ligase in overseeing the assembly of a key cellular complex.
History
DepositionJul 28, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15485.png

Downloads & links

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Map

FileDownload / File: emd_15485.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally sharpened map (LocScale).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 304.2 Å		0.85 Å/pix.
x 360 pix.
= 304.2 Å		0.85 Å/pix.
x 360 pix.
= 304.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.15890203 - 0.67017674
Average (Standard dev.)0.0010420822 (±0.013839088)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 304.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Full map.

Fileemd_15485_additional_1.map
AnnotationFull map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15485_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15485_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of DDB1-DCAF12

EntireName: Complex of DDB1-DCAF12
Components
  • Complex: Complex of DDB1-DCAF12
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DDB1- and CUL4-associated factor 12

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Supramolecule #1: Complex of DDB1-DCAF12

SupramoleculeName: Complex of DDB1-DCAF12 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.784258 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSSHHHHHH SAVDENLYFQ GGGRMSYNYV VTAQKPTAVN GCVTGHFTSA EDLNLLIAKN TRLEIYVVTA EGLRPVKEVG MYGKIAVME LFRPKGESKD LLFILTAKYN ACILEYKQSG ESIDIITRAH GNVQDRIGRP SETGIIGIID PECRMIGLRL Y DGLFKVIP ...String:
MGSSHHHHHH SAVDENLYFQ GGGRMSYNYV VTAQKPTAVN GCVTGHFTSA EDLNLLIAKN TRLEIYVVTA EGLRPVKEVG MYGKIAVME LFRPKGESKD LLFILTAKYN ACILEYKQSG ESIDIITRAH GNVQDRIGRP SETGIIGIID PECRMIGLRL Y DGLFKVIP LDRDNKELKA FNIRLEELHV IDVKFLYGCQ APTICFVYQD PQGRHVKTYE VSLREKEFNK GPWKQENVEA EA SMVIAVP EPFGGAIIIG QESITYHNGD KYLAIAPPII KQSTIVCHNR VDPNGSRYLL GDMEGRLFML LLEKEEQMDG TVT LKDLRV ELLGETSIAE CLTYLDNGVV FVGSRLGDSQ LVKLNVDSNE QGSYVVAMET FTNLGPIVDM CVVDLERQGQ GQLV TCSGA FKEGSLRIIR NGIGIHEHAS IDLPGIKGLW PLRSDPNRET DDTLVLSFVG QTRVLMLNGE EVEETELMGF VDDQQ TFFC GNVAHQQLIQ ITSASVRLVS QEPKALVSEW KEPQAKNISV ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEH EVA CLDITPLGDS NGLSPLCAIG LWTDISARIL KLPSFELLHK EMLGGEIIPR SILMTTFESS HYLLCALGDG ALFYFGL NI ETGLLSDRKK VTLGTQPTVL RTFRSLSTTN VFACSDRPTV IYSSNHKLVF SNVNLKEVNY MCPLNSDGYP DSLALANN S TLTIGTIDEI QKLHIRTVPL YESPRKICYQ EVSQCFGVLS SRIEVQDTSG GTTALRPSAS TQALSSSVSS SKLFSSSTA PHETSFGEEV EVHNLLIIDQ HTFEVLHAHQ FLQNEYALSL VSCKLGKDPN TYFIVGTAMV YPEEAEPKQG RIVVFQYSDG KLQTVAEKE VKGAVYSMVE FNGKLLASIN STVRLYEWTT EKELRTECNH YNNIMALYLK TKGDFILVGD LMRSVLLLAY K PMEGNFEE IARDFNPNWM SAVEILDDDN FLGAENAFNL FVCQKDSAAT TDEERQHLQE VGLFHLGEFV NVFCHGSLVM QN LGETSTP TQGSVLFGTV NGMIGLVTSL SESWYNLLLD MQNRLNKVIK SVGKIEHSFW RSFHTERKTE PATGFIDGDL IES FLDISR PKMQEVVANL QYDDGSGMKR EATADDLIKV VEELTRIH

UniProtKB: DNA damage-binding protein 1

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Macromolecule #2: DDB1- and CUL4-associated factor 12

MacromoleculeName: DDB1- and CUL4-associated factor 12 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.373191 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDWSHPQFEK SAVDENLYFQ GGGRMARKVV SRKRKAPASP GAGSDAQGPQ FGWDHSLHKR KRLPPVKRSL VYYLKNREVR LQNETSYSR VLHGYAAQQL PSLLKEREFH LGTLNKVFAS QWLNHRQVVC GTKCNTLFVV DVQTSQITKI PILKDREPGG V TQQGCGIH ...String:
MDWSHPQFEK SAVDENLYFQ GGGRMARKVV SRKRKAPASP GAGSDAQGPQ FGWDHSLHKR KRLPPVKRSL VYYLKNREVR LQNETSYSR VLHGYAAQQL PSLLKEREFH LGTLNKVFAS QWLNHRQVVC GTKCNTLFVV DVQTSQITKI PILKDREPGG V TQQGCGIH AIELNPSRTL LATGGDNPNS LAIYRLPTLD PVCVGDDGHK DWIFSIAWIS DTMAVSGSRD GSMGLWEVTD DV LTKSDAR HNVSRVPVYA HITHKALKDI PKEDTNPDNC KVRALAFNNK NKELGAVSLD GYFHLWKAEN TLSKLLSTKL PYC RENVCL AYGSEWSVYA VGSQAHVSFL DPRQPSYNVK SVCSRERGSG IRSVSFYEHI ITVGTGQGSL LFYDIRAQRF LEER LSACY GSKPRLAGEN LKLTTGKGWL NHDETWRNYF SDIDFFPNAV YTHCYDSSGT KLFVAGGPLP SGLHGNYAGL WS

UniProtKB: DDB1- and CUL4-associated factor 12

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 431000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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